Rapid diagnostic tests (RDTs) for HIV antibodies remain the primary method of diagnosis of HIV in individuals over age 18 months in Lesotho. Although antibody tests have high sensitivity and specificity, up to 2.3% of serial two-test algorithms can have discrepant results between RDTs. In the case of inconclusive RDT results, Lesotho guidelines at the time of this study recommended either repeat testing with the same RDT algorithm after 14 days or immediately collect a blood sample to be sent for laboratory-based polymerase chain reaction testing. Point-of-care qualitative nucleic acid tests (POC qual NAT) may have benefits in rapidly resolving these inconclusive results, particularly when compared with repeating RDTs later or conventional polymerase chain reaction testing at the National Reference Laboratory. Hospitals and clinics at 29 locations throughout Lesotho that had access to point-of-care nucleic acid testing. Retrospective case review. We identified 100 testing records where POC qual NAT was used to resolve inconclusive RDTs per Lesotho guidelines. Eighty-nine percent of patients received their results in a median of one day from their inconclusive RDT result (interquartile range 0-7 days). Sixty-eight patients (68%) were determined to be HIV positive based on POC nucleic acid tests (NATs), of which 54 (79%) were started on antiretroviral therapy (ART). Median time from inconclusive RDT result to initiation of ART therapy was 2 days (interquartile range 0-14 days). Three patients in this review were pregnant at the time of testing; one was HIV positive by POC qual NAT and was started on ART therapy the same day. As the availability of POC qual NAT platforms increases, they may serve as feasible options for rapid resolution of inconclusive results and initiation of ART, particularly in populations with high risk of imminent transmission.